Mercurial > repos > mvdbeek > bam_readtagger

annotate filter_insertions.xml @ 38:f6311a04a6c9 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
author mvdbeek
date Thu, 15 Mar 2018 05:13:22 -0400
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children 432bb619c079
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38
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9">
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mvdbeek
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2 <description>based on softclips in control files</description>
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mvdbeek
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.4.9">readtagger</requirement>
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mvdbeek
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5 </requirements>
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mvdbeek
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6 <version_command>confirm_insertions --version</version_command>
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mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[
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mvdbeek
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8 confirm_insertions
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mvdbeek
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9 --putative_insertions_path '$putative_insertions'
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mvdbeek
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10 --all_treatments_path '$all_insertions'
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mvdbeek
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11 --all_controls_path '$all_controls'
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mvdbeek
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12 --output_path '$output'
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mvdbeek
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13 $output_discard
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mvdbeek
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14 ]]></command>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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15 <inputs>
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mvdbeek
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16 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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17 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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18 <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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19 <param name="output_discard" label="Output discarded records? Thye will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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20 </inputs>
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mvdbeek
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21 <outputs>
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mvdbeek
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22 <data name="output" format="gff3"/>
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mvdbeek
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23 </outputs>
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mvdbeek
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24 <tests>
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mvdbeek
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25 <test>
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mvdbeek
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26 <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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27 <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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28 <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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29 <output name="output" file="confirmed_insertions.gff" ftype="gff3"/>
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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30 </test>
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mvdbeek
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31 </tests>
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32 <help><![CDATA[
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mvdbeek
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33 .. code-block::
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34
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35
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36 Usage: confirm_insertions [OPTIONS]
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37
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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38 Confirm insertions by checking that control file does not contain the same
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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39 clipping pattern.
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mvdbeek
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40
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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41 Options:
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42 -p, --putative_insertions_path PATH
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43 Path to file containing putative somatic
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
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44 insertions [required]
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
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45 -t, --all_treatments_path PATH Path to file containing all treatment
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46 insertions [required]
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mvdbeek
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47 -c, --all_controls_path PATH Path to file containing all control
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mvdbeek
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48 insertions [required]
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mvdbeek
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49 -o, --output_path TEXT Write annotated output to this Path.
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50 --output_discarded_records / --no_output_discarded_records
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51 Discard an alternative flag if the current
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mvdbeek
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52 read is in a proper pair.
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mvdbeek
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53 --version Show the version and exit.
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mvdbeek
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54 --help Show this message and exit.
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mvdbeek
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55 ]]></help>
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56 </tool>